Sick koi?

My yellow koi has developed these black spots all over her back. It's been at least 3-4 weeks, with no sign of improvement. She used to just have clear, clean looking yellow scales. Her behavior has not changed at all, still the leader of the pack, eating and swimming as normal.
I searched quite a bit, and the only thing I found was Koi Black Spot- http://www.inlandkoi.com/koidisease.html
But I am unsure if it is correct. It's supposed to be fading away within 6 weeks, but I see no change.

So I was not worried, but now as winter is racing up to us, I'm worried this will compromise her immune system. Any ideas as to what this could be? Or what I can do to help it?

I have been fortunate in that I have not had to deal with sick fish. I read about the black spot from the link you provided and it says they should be small black specks. This looks more like a fungal disease or something. Looked really closely at the picture and does not look like normal color changes to me. I would say consult the person you purchased the fish from to get their recommendation. There are some things that treat a pretty broad spectrum of problems but I do not have any personal experience with them.

Thank you for your reply tetley. I'll go show this picture to the place I bought her. It's worrying that you think it is fungal...but I agree they are not small dots.
Anyone else recognize this as anything they've seen?

Guy at the store that sold me June, said that it is probably Shimi, which is a genetic weakness that comes out when trauma or bad water conditions exist.

http://www.2uv.com/html/articles/articles_details.php?article_id=103&category=17&name=Diseases

June jumped out of the pond (I assume) earlier in the summer and was on the verge of death, swimming upsidedown, when I found her, so I held her in a quarantine tank over an oxygenator for 3 hours until she swam upright. When the koi guy heard that story, the shimi made more sense to him. Also, I've had high pH readings in my pond all summer. He said to watch it a little longer and it should go away.